Relations in Anatomy and Image Ontologies

Dirk Marwede

Institute for Formal Ontology and Medical Information Science, Saarland University, Saarbruecken, Germany

Department of Diagnostic Radiology, Leipzig University, Germany

Overview

• OBO relation ontology

• Anatomical Entities (Foundational Model of Anatomy, FMA)

– Relations in Anatomy Ontology

• Diagnostic Domain of Medial Imaging

– Image Entity Types

– Relations between Image Entity Types

– Building an Imaging Ontology (RadiO)

OBO relation ontology• Three types of binary relations

– < class, class >: e.g. is_a lung is_a lobular organ

– < instance, class >: instance_ofThis particular „lung“ instance_of class lung

– < instance, instance >: instance-level relation, e.g. part_ofThis particular instance of „right lower lobe of lung“ part_of this

particular instance of „right lung“

• Relations between classes represent what is general in reality. – class level:

• lung is_a lobular organ

– instance level: • this particular instance of lung is_a particular instance of lobular organ

Anatomical Ontologies (FMA)

• Class level-relations

– Structural Relationships between Anatomical Entities

• Boundary (bounded_by)

• Partonomy (part_of, regional_part_of, constitutional_part_of,…)

• Spatial Association

– Location (located_in, contained_in, adjecent_to)– Orientation (coordinate, laterality)– Connectivity (continuous_with, attached_to)

– Properties of Anatomical Entities:

• Dimension • Physical Properties

Canonical Anatomical Entity - Lung

Image Ontologies

• Medical Imaging is concerned with diagnosing diseases.

• How we come from an image to a diagnosis?

– What kind of entities exist on the image and how do they relate to each other ?

• Image Entity Types

– Anatomical Image Entities

– Pathological Image Entities

– Image Features

dependent entities

Imaging body entites

Image Entity Types – Anatomical Image Entities

Image Entity Types – Pathological Image Entity

• Which diseases can be inferred from images?

• What kind of image features do diseases have?

• Does a disease have in any case identical image features?

• If not, what are criteria which give evidence for a disease?

Pathological Image Entities

Features

Class-Level Relations between Image Entity Types

• C image_of C1 – basic relation holding between two continuants. – C is an anatomical or pathological image entity, C1 is an anatomical or

pathological entity.

• C has_feature C1 – a property relation holding between two continuants. – C is an anatomical or pathological image entity, C1 is a feature attribute.

• C has_location C1 – basic location relation holding between two continuants. – C is a visual feature or pathological image entity and C1 is an anatomical

image entity

Class-level relations between Image Entity Types and the FMA

has_feature

Anatomical Image Entityimage_of

Anatomical Entity (FMA)

Pathological Image EntityFeature

has_location

has_feature

has_location

Subrelations of has_feature Relations to annotate properties to anatomical and pathological image entities

Visual features

Morphology featuresc has_shape c1 at time of examination.

Adrenal gland [Anatomic Image Entity] has_shape round [Attribute:Shape] at time of examination

c has_size c1 at time of examination.T1 vertebral body [Anatomical Image Entity] has_size decreased in height [Attribute:Size] at time of examination

c has_composition c1 at time of examination.Tumor [Pathological Image Entity] has_composition cystic [Attribute:Composition] at time of examination

Signal features

c has_density c1 at time of examination.Liver [Anatomical Image Entity] has_density hypodense [Attribute:Density] at time of examination (or contrast phase).

General features

c has_amount c1 at time of examination.Pulmonary nodule [Pathological Image Entity] has_amount multiple [Attribute:Amount] at time of examination.

Use of Relations in Medical Imaging [Pathological Image Entity] has_feature [GeneralFeature]

Pulmonary embolism has_timing acute

[Pathological Image Entity] has_location [Anatomical Image Entity]has_feature [MorphologyFeature]

Mass has_location upper right lobe of right lunghas_margin spiculatedhas_shape roundhas_composition solid

evidence for malignant neoplasm

[Anatomical Image Entity] has_feature [MorphologyFeature]

Thyroid gland has_size enlarged

[Anatomical Image Entity] has_feature [MorphologyFeature][Pathological Image Entity] has_location [Anatomical Image Entity]

Hilar lymph node has_composition calcifiedGranuloma has_location upper lobe of left lung

evidence for tuberculosis has_timing old

Disease Ontology

Imaging Ontology

Imaging Ontology

Imaging Ontology ?

Disease Ontology

Conclusions• Entities of two domains

– Body Entities– Image Entities (dependent entities)

• Construction of an Imaging Ontology

– Image Entity Types

• Anatomical Image entities • Pathological Image Entities • Features

– Class level relations between Image Entity Types (and the FMA)

• Application Ontology (RadiO) for Diagnostic Domain

– Annotating image features to Anatomical and Pathological Image entities.

– Criteria for Pathological Image Entities: Tracking the use of relations between image entity types to discriminate image features of diseases.

• Separating/linking of an Imaging Ontology from/to other Ontologies of Diseases/Diagnosis.

Thank you!

Matthew FieldingBarry SmithDaniel Rubin

RadLex Committee